Update assets (#51)

* update GATK bundle assets

* Update assets/genomes/generate_yaml_asset.sh

Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>

* move files

* keep existing assets

* add fasta_fai

* fix fasta

* fix files

* add fasta_dict

* add fasta_fai

* update CHANGELOG

---------

Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>

.gitignore

@@ -12,3 +12,5 @@ null/
 tmp/
 .nf-test
 .vscode
+assets/all_*.txt
+assets/ngi-igenomes_file_manifest.txt

CHANGELOG.md

@@ -24,6 +24,7 @@ Initial release of nf-core/references, created with the [nf-core](https://nf-co.
 - [42](https://github.com/nf-core/references/pull/42) - Add multiple references build tests
 - [43](https://github.com/nf-core/references/pull/43) - Add support for multiple known_indels_vcf via s3 globs
 - [47](https://github.com/nf-core/references/pull/47) - Add fasta assets for files in igenomes
+- [51](https://github.com/nf-core/references/pull/51) - Add fasta_fai assets for files in igenomes
 
 ### Changed
 
@@ -51,6 +52,7 @@ Initial release of nf-core/references, created with the [nf-core](https://nf-co.
 - [36](https://github.com/nf-core/references/pull/36) - Deal intervals generation
 - [39](https://github.com/nf-core/references/pull/39) - Fix gtf generation and dependencies
 - [50](https://github.com/nf-core/references/pull/50) - Minimal JAVA is 17
+- [51](https://github.com/nf-core/references/pull/51) - Fix missing fasta assets for GATK build
 
 ### Dependencies
 

assets/generate_yaml_asset.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+
+# Download or regenerate manifest file
+
+# cf https://github.com/ewels/AWS-iGenomes/pull/22
+
+# wget https://raw.githubusercontent.com/ewels/AWS-iGenomes/refs/heads/master/ngi-igenomes_file_manifest.txt
+
+# aws s3 --no-sign-request ls --recursive s3://ngi-igenomes/igenomes/ | cut -d "/" -f 2- > tmp
+# for i in `cat tmp`; do
+#     echo s3://ngi-igenomes/igenomes/$i >> manifest
+# done
+# mv manifest ngi-igenomes_file_manifest.txt
+# rm tmp
+
+# Remove existing assets
+rm -rf igenomes/
+
+# Generate base info in species/genome/build.yml
+
+# All source fasta.fai
+# ALL fais are coming from a fasta file of the same name
+# Hence I use it to generate fasta + fai (and catch with that the fasta that are not following the gemome.fa name scheme)
+
+cat ngi-igenomes_file_manifest.txt | grep "\.fai" | grep -v "Bowtie2Index" | grep -v "fai\.gz" > all_fai.txt
+
+for i in `cat all_fai.txt`;
+do
+    species=$(echo $i | cut -d "/" -f 5)
+    genome=$(echo $i | cut -d "/" -f 6)
+    build=$(echo $i | cut -d "/" -f 7)
+
+    mkdir -p igenomes/${species}/${genome}
+    if [ -f "igenomes/${species}/${genome}/${build}.yml" ]; then
+        build+="_2_"
+    fi
+    echo "- genome: '${build}'" > igenomes/${species}/${genome}/${build}.yml
+    echo "  fasta: '${i::-4}'" >> igenomes/${species}/${genome}/${build}.yml
+    echo "  source: '${genome}'" >> igenomes/${species}/${genome}/${build}.yml
+    echo "  species:  '${species}'" >> igenomes/${species}/${genome}/${build}.yml
+    echo "  fasta_fai: '${i}'" >> igenomes/${species}/${genome}/${build}.yml
+done
+
+# # All source fasta.dict
+# cat ngi-igenomes_file_manifest.txt | grep "\.dict" | grep -v "dict\.gz" | grep -v "dict\.old" > all_dict.txt
+
+# # Generate base info in species/genome/build.yml
+
+# for i in `cat all_dict.txt`;
+# do
+#     species=$(echo $i | cut -d "/" -f 5)
+#     genome=$(echo $i | cut -d "/" -f 6)
+#     build=$(echo $i | cut -d "/" -f 7)
+
+#     echo "  fasta_dict: '${i}'" >> igenomes/${species}/${genome}/${build}.yml
+# done
+
+#  Homo_sapiens/GATK/GRCh37.yml should actually be Homo_sapiens/GATK/GRCh37decoy.yml
+mv igenomes/Homo_sapiens/GATK/GRCh37.yml igenomes/Homo_sapiens/GATK/GRCh37decoy.yml

assets/genomes/Mus_musculus/NCBI/GRCm39.yml → assets/genomes/Mus_musculus/NCBI/mm39.yml

@@ -1,4 +1,4 @@
-- genome: GRCm39
+- genome: mm39
   fasta: https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz
   gtf: https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/genes/mm39.ncbiRefSeq.gtf.gz
   mito_name: MT

assets/genomes/Arabidopsis_thaliana/Ensembl/TAIR10.yml → assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Arabidopsis_thaliana"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Arabidopsis_thaliana/Ensembl/TAIR9.yml → assets/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Arabidopsis_thaliana"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR9/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Arabidopsis_thaliana/NCBI/TAIR10.yml → assets/igenomes/Arabidopsis_thaliana/NCBI/TAIR10.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Arabidopsis_thaliana"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/TAIR10/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Arabidopsis_thaliana/NCBI/build9.1.yml → assets/igenomes/Arabidopsis_thaliana/NCBI/build9.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Arabidopsis_thaliana"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/NCBI/build9.1/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13.yml → assets/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Bacillus_cereus_ATCC_10987"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bacillus_cereus_ATCC_10987/NCBI/2004-02-13/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bacillus_subtilis_168/Ensembl/EB2.yml → assets/igenomes/Bacillus_subtilis_168/Ensembl/EB2.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Bacillus_subtilis_168"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/Ensembl/Btau_4.0.yml → assets/igenomes/Bos_taurus/Ensembl/Btau_4.0.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/Btau_4.0/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/Ensembl/UMD3.1.yml → assets/igenomes/Bos_taurus/Ensembl/UMD3.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/NCBI/Btau_4.2.yml → assets/igenomes/Bos_taurus/NCBI/Btau_4.2.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.2/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/NCBI/Btau_4.6.1.yml → assets/igenomes/Bos_taurus/NCBI/Btau_4.6.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/Btau_4.6.1/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/NCBI/UMD_3.1.1.yml → assets/igenomes/Bos_taurus/NCBI/UMD_3.1.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1.1/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/NCBI/UMD_3.1.yml → assets/igenomes/Bos_taurus/NCBI/UMD_3.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/NCBI/UMD_3.1/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/UCSC/bosTau4.yml → assets/igenomes/Bos_taurus/UCSC/bosTau4.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau4/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/UCSC/bosTau6.yml → assets/igenomes/Bos_taurus/UCSC/bosTau6.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau6/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/UCSC/bosTau7.yml → assets/igenomes/Bos_taurus/UCSC/bosTau7.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau7/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Bos_taurus/UCSC/bosTau8.yml → assets/igenomes/Bos_taurus/UCSC/bosTau8.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Bos_taurus"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Caenorhabditis_elegans/Ensembl/WBcel215.yml → assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Caenorhabditis_elegans"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel215/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Caenorhabditis_elegans/Ensembl/WBcel235.yml → assets/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Caenorhabditis_elegans"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Caenorhabditis_elegans/Ensembl/WS210.yml → assets/igenomes/Caenorhabditis_elegans/Ensembl/WS210.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Caenorhabditis_elegans"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS210/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Caenorhabditis_elegans/Ensembl/WS220.yml → assets/igenomes/Caenorhabditis_elegans/Ensembl/WS220.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Caenorhabditis_elegans"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WS220/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Caenorhabditis_elegans/NCBI/WS190.yml → assets/igenomes/Caenorhabditis_elegans/NCBI/WS190.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Caenorhabditis_elegans"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS190/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Caenorhabditis_elegans/NCBI/WS195.yml → assets/igenomes/Caenorhabditis_elegans/NCBI/WS195.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Caenorhabditis_elegans"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/NCBI/WS195/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Caenorhabditis_elegans/UCSC/ce10.yml → assets/igenomes/Caenorhabditis_elegans/UCSC/ce10.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Caenorhabditis_elegans"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Caenorhabditis_elegans/UCSC/ce6.yml → assets/igenomes/Caenorhabditis_elegans/UCSC/ce6.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce6/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Caenorhabditis_elegans"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce6/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Canis_familiaris/Ensembl/BROADD2.yml → assets/igenomes/Canis_familiaris/Ensembl/BROADD2.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/BROADD2/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Canis_familiaris"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/BROADD2/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Canis_familiaris/Ensembl/CanFam3.1.yml → assets/igenomes/Canis_familiaris/Ensembl/CanFam3.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Canis_familiaris"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Canis_familiaris/NCBI/build2.1.yml → assets/igenomes/Canis_familiaris/NCBI/build2.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build2.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Canis_familiaris"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build2.1/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Canis_familiaris/NCBI/build3.1.yml → assets/igenomes/Canis_familiaris/NCBI/build3.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build3.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Canis_familiaris"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Canis_familiaris/NCBI/build3.1/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Canis_familiaris/UCSC/canFam2.yml → assets/igenomes/Canis_familiaris/UCSC/canFam2.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam2/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Canis_familiaris"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam2/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Canis_familiaris/UCSC/canFam3.yml → assets/igenomes/Canis_familiaris/UCSC/canFam3.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Canis_familiaris"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Danio_rerio/Ensembl/GRCz10.yml → assets/igenomes/Danio_rerio/Ensembl/GRCz10.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Danio_rerio"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Danio_rerio/Ensembl/Zv9.yml → assets/igenomes/Danio_rerio/Ensembl/Zv9.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/Zv9/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Danio_rerio"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/Zv9/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Danio_rerio/NCBI/GRCz10.yml → assets/igenomes/Danio_rerio/NCBI/GRCz10.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Danio_rerio"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/GRCz10/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Danio_rerio/NCBI/Zv9.yml → assets/igenomes/Danio_rerio/NCBI/Zv9.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/Zv9/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Danio_rerio"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Danio_rerio/NCBI/Zv9/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Danio_rerio/UCSC/danRer10.yml → assets/igenomes/Danio_rerio/UCSC/danRer10.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Danio_rerio"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Danio_rerio/UCSC/danRer7.yml → assets/igenomes/Danio_rerio/UCSC/danRer7.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer7/Sequence/WholeGenomeFasta/genome.fa"
   source: "UCSC"
   species: "Danio_rerio"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer7/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Drosophila_melanogaster/Ensembl/BDGP5.25.yml → assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Drosophila_melanogaster"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Drosophila_melanogaster/Ensembl/BDGP5.yml → assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP5.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Drosophila_melanogaster"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP5/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Drosophila_melanogaster/Ensembl/BDGP6.yml → assets/igenomes/Drosophila_melanogaster/Ensembl/BDGP6.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
   source: "Ensembl"
   species: "Drosophila_melanogaster"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa.fai"

assets/genomes/Drosophila_melanogaster/NCBI/build4.1.yml → assets/igenomes/Drosophila_melanogaster/NCBI/build4.1.yml

@@ -2,3 +2,4 @@
   fasta: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build4.1/Sequence/WholeGenomeFasta/genome.fa"
   source: "NCBI"
   species: "Drosophila_melanogaster"
+  fasta_fai: "s3://ngi-igenomes/igenomes/Drosophila_melanogaster/NCBI/build4.1/Sequence/WholeGenomeFasta/genome.fa.fai"